Monitoring Bacterial Biodiversity in Surface Sediment Using Terminal Restriction Fragment Length Polymorphism Analysis (T-RFLP): Application to Coastal Environment

By using traditional bacterial culture methods, only less than 1% of bacteria from environmental samples can be cultivated for biodiversity and microbial ecology studies. In recent years, however, rapid development in molecular biology and ecology has enabled us to explore genetic diversity of bacteria in environmental samples using culture-independent approaches. For example, the recent emergence of (ribosomal DNA) terminal restriction fragment length polymorphism (T-RFLP) analysis has made it become feasible to investigate bacterial diversity more accurately, reliably, speedily and at cheaper cost in coastal sediment samples. This brief paper provides an overview of pros and cons of the molecular approach, T-RFLP, in analyzing the diversity of bacteria in surface sediments of contrasting coastal environments in sub-tropical region. We used the terminal restriction fragment length polymorphism (T-RFLP) analysis to track the changes of bacterial community compositions in surface sediments collected from five sites along a pollution gradient at six sampling occasions (2004 to 2006) in subtropical Hong Kong waters. Our application of this technique in coastal environments illustrates the feasibility and the power of this novel approach for environmental monitoring and ecosystem recovery studies.